General Structure Information
| PDB ID | 3eg9 |
| HGNC Gene Label(s) | SEC24D |
| Structure Name | crystal structure of the mammalian copii-coat protein sec23/24 bound to the transport signal sequence of membrin |
| Resolution | 3.0Å |
| Reference | AUTH J.D.MANCIAS,J.GOLDBERGTITL STRUCTURAL BASIS OF CARGO MEMBRANE PROTEIN DISCRIMINATION BYTITL 2 THE HUMAN COPII COAT MACHINERY.REF EMBO J. V. 27 2918 2008REFN ISSN 0261-4189PMID 18843296DOI 10.1038/EMBOJ.2008.208 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 764 |
| Number Of SNVs | 171 |
| Number Of Permutations | 71782 |
| Optimal Distance Threshold | 10.0 |
| K Statistic | 0.023 |
| p-value | 0.875 |
COSMIC
| Number Of Residues | 764 |
| Number Of SNVs | 6 |
| Number Of Permutations | 1287 |
| Optimal Distance Threshold | 14.0 |
| K Statistic | 0.133 |
| p-value | 0.791 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 171 |
| Number Of COSMIC SNVs | 5 |
| Optimal Distance Threshold | 14.0 |
| K Statistic | 0.139 |
| p-value | 0.73 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:119736185 | P>S | B:268 | (-63.48, -13.30, 3.60) | |
| 4:119727097 | E>K | B:273 | (-56.20, -16.11, 7.82) | |
| 4:119727089 | rs115571066 | D>E | B:275 | (-52.33, -15.97, 1.12) |
| 4:119727081 | S>T | B:278 | (-48.79, -19.78, 2.11) | |
| 4:119727078 | R>K | B:279 | (-47.59, -16.25, -1.17) | |
| 4:119727079 | R>G | B:279 | (-47.59, -16.25, -1.17) | |
| 4:119727075 | G>E | B:280 | (-45.87, -15.08, 4.03) | |
| 4:119727072 | G>E | B:281 | (-42.69, -14.40, 5.01) | |
| 4:119727070 | Q>E | B:282 | (-42.35, -16.47, 1.93) | |
| 4:119727038 | rs371009255 | I>M | B:292 | (-50.10, -15.31, -9.48) |
| 4:119727040 | I>L | B:292 | (-50.10, -15.31, -9.48) | |
| 4:119727033 | rs377693234 | P>L | B:294 | (-49.28, -12.15, -3.24) |
| 4:119727028 | V>I | B:296 | (-53.09, -6.69, -0.79) | |
| 4:119727021 | T>K | B:298 | (-50.22, -10.89, 2.28) | |
| 4:119727017 | D>E | B:299 | (-47.20, -8.59, 4.94) | |
| 4:119727016 | C>S | B:300 | (-44.38, -10.04, 1.55) | |
| 4:119718962 | rs369541638 | N>S | B:307 | (-41.44, -8.39, -13.66) |
| 4:119718941 | rs148676365 | R>H | B:314 | (-51.66, -6.09, -7.46) |
| 4:119718942 | rs561087748 | R>C | B:314 | (-51.66, -6.09, -7.46) |
| 4:119718914 | rs199527760 | T>M | B:323 | (-58.87, -14.07, -28.52) |
| 4:119718903 | rs376572075 | A>S | B:327 | (-62.76, -12.30, -23.62) |
| 4:119718893 | A>D | B:330 | (-65.56, -14.51, -19.87) | |
| 4:119718878 | A>V | B:335 | (-57.03, -4.53, -15.77) | |
| 4:119718840 | rs572183269 | E>K | B:348 | (-38.57, -3.60, -0.09) |
| 4:119689456 | rs202241579 | Y>C | B:352 | (-31.29, 1.63, -8.80) |
| 4:119689451 | rs368921282 | V>L | B:354 | (-31.10, 5.62, -15.61) |
| 4:119689417 | rs189735385 | N>S | B:365 | (-37.87, 4.66, -33.34) |
| 4:119689418 | N>H | B:365 | (-37.87, 4.66, -33.34) | |
| 4:119689398 | M>I | B:371 | (-34.45, 0.22, -22.85) | |
| 4:119689400 | M>V | B:371 | (-34.45, 0.22, -22.85) | |
| 4:119689387 | M>T | B:375 | (-35.99, -4.59, -25.51) | |
| 4:119689370 | rs146307367 | G>R | B:381 | (-25.64, -5.96, -30.08) |
| 4:119689366 | R>K | B:382 | (-23.93, -4.76, -34.14) | |
| 4:119689333 | rs372226200 | N>S | B:393 | (-34.26, -0.55, -32.95) |
| 4:119686060 | COSM585621 | Y>C | B:399 | (-26.96, 1.40, -24.29) |
| 4:119686058 | F>V | B:400 | (-22.33, -2.06, -28.44) | |
| 4:119686052 | rs140080517 | H>Y | B:402 | (-19.99, -7.09, -26.93) |
| 4:119686040 | I>V | B:406 | (-28.62, -16.93, -24.95) | |
| 4:119686024 | D>G | B:411 | (-24.65, -4.72, -19.46) | |
| 4:119686018 | Y>C | B:413 | (-27.81, -9.43, -13.79) | |
| 4:119685984 | rs368390247 | E>D | B:424 | (-36.62, 6.85, -12.10) |
| 4:119685973 | T>I | B:428 | (-33.88, 15.18, -21.90) | |
| 4:119685968 | rs371378788 | D>Y | B:430 | (-36.67, 16.78, -25.27) |
| 4:119685962 | C>R | B:432 | (-39.26, 19.90, -20.91) | |
| 4:119678999 | rs201158359 | K>R | B:434 | (-41.55, 26.53, -22.64) |
| 4:119678963 | rs376313937 | M>T | B:446 | (-55.89, 29.06, -0.35) |
| 4:119678959 | I>M | B:447 | (-57.24, 30.38, 4.95) | |
| 4:119678960 | I>T | B:447 | (-57.24, 30.38, 4.95) | |
| 4:119678915 | COSM1050371 | I>T | B:462 | (-55.06, 26.69, 9.92) |
| 4:119678897 | T>N | B:468 | (-45.07, 23.83, 13.14) | |
| 4:119678880 | P>S | B:474 | (-40.89, 18.62, 1.34) | |
| 4:119674037 | E>D | B:477 | (-30.29, 13.58, 0.80) | |
| 4:119674026 | T>M | B:481 | (-33.27, 24.17, 1.66) | |
| 4:119674014 | rs200867651 COSM1050370 COSM1186638 |
R>Q | B:485 | (-41.31, 29.58, -4.33) |
| 4:119674003 | rs138187019 | I>L | B:489 | (-54.53, 33.50, 0.06) |
| 4:119673996 | Y>F | B:491 | (-61.20, 32.58, 1.00) | |
| 4:119673951 | Q>P | B:506 | (-45.34, 45.11, 8.34) | |
| 4:119673930 | T>I | B:513 | (-62.95, 43.12, -4.88) | |
| 4:119673931 | T>A | B:513 | (-62.95, 43.12, -4.88) | |
| 4:119673925 | V>I | B:515 | (-64.69, 38.35, -8.18) | |
| 4:119673921 | G>E | B:516 | (-64.56, 37.19, -12.18) | |
| 4:119673916 | rs369026913 | V>L | B:518 | (-59.69, 37.11, -10.77) |
| 4:119673900 | L>W | B:523 | (-44.47, 38.86, -8.95) | |
| 4:119673889 | rs141180741 | L>F | B:527 | (-44.39, 32.51, -4.23) |
| 4:119673874 | E>Q | B:532 | (-34.76, 33.17, 3.47) | |
| 4:119673867 | Q>P | B:534 | (-38.97, 32.33, 9.53) | |
| 4:119673242 | L>S | B:540 | (-49.30, 36.81, 8.33) | |
| 4:119673228 | P>A | B:545 | (-56.13, 35.15, 13.46) | |
| 4:119673213 | D>H | B:550 | (-64.60, 40.90, 14.76) | |
| 4:119673192 | V>I | B:557 | (-65.91, 32.84, -3.23) | |
| 4:119673183 | P>S | B:560 | (-62.39, 32.57, -7.57) | |
| 4:119673180 | rs569603974 | V>F | B:561 | (-59.61, 30.75, -4.87) |
| 4:119673177 | I>V | B:562 | (-59.00, 27.38, -7.76) | |
| 4:119666214 | A>V | B:571 | (-46.65, 33.77, -13.23) | |
| 4:119666215 | A>T | B:571 | (-46.65, 33.77, -13.23) | |
| 4:119666209 | D>H | B:573 | (-43.27, 29.66, -15.09) | |
| 4:119666170 | P>T | B:586 | (-70.11, 28.57, -2.47) | |
| 4:119666157 | A>V | B:590 | (-69.34, 34.52, -8.71) | |
| 4:119666133 | rs375796795 | D>V | B:598 | (-80.37, 18.45, -2.71) |
| 4:119666112 | rs200495446 | T>I | B:605 | (-84.60, 9.72, -12.17) |
| 4:119666109 | D>A | B:606 | (-82.52, 8.29, -16.15) | |
| 4:119665311 | rs373049214 | I>M | B:610 | (-77.62, 15.96, -12.75) |
| 4:119665297 | rs572876070 | Q>L | B:615 | (-74.16, 23.44, -9.83) |
| 4:119665285 | Y>C | B:619 | (-66.31, 24.44, -10.71) | |
| 4:119665283 | D>N | B:620 | (-64.77, 20.83, -15.94) | |
| 4:119665279 | S>L | B:621 | (-62.90, 24.84, -17.29) | |
| 4:119665273 | A>V | B:623 | (-59.51, 22.02, -14.33) | |
| 4:119665262 | COSM4121572 | V>M | B:627 | (-53.96, 20.46, -15.84) |
| 4:119665253 | G>S | B:630 | (-49.51, 22.56, -12.93) | |
| 4:119665246 | S>C | B:632 | (-52.84, 20.74, -7.76) | |
| 4:119665213 | V>A | B:643 | (-71.30, 21.81, 0.40) | |
| 4:119665201 | rs374055733 COSM3007672 |
S>L | B:647 | (-68.87, 20.94, -7.36) |
| 4:119665193 | L>M | B:650 | (-64.43, 18.32, -10.29) | |
| 4:119665153 | N>S | B:663 | (-68.85, 16.20, 8.41) | |
| 4:119665151 | N>H | B:664 | (-70.57, 18.82, 11.67) | |
| 4:119662174 | Q>E | B:673 | (-59.24, 13.87, 11.93) | |
| 4:119662171 | F>V | B:674 | (-57.07, 19.26, 9.97) | |
| 4:119662146 | I>T | B:682 | (-47.34, 18.92, 3.89) | |
| 4:119662131 | G>A | B:687 | (-45.29, 15.05, -8.17) | |
| 4:119662120 | I>V | B:691 | (-47.81, 12.71, -18.71) | |
| 4:119662107 | R>H | B:695 | (-46.25, 3.10, -23.99) | |
| 4:119661955 | rs368665619 | A>T | B:702 | (-55.11, 1.36, -23.34) |
| 4:119661939 | G>A | B:707 | (-58.89, 8.68, -11.68) | |
| 4:119661924 | N>S | B:712 | (-57.34, 16.36, -23.21) | |
| 4:119661921 | rs146773641 | N>T | B:713 | (-55.68, 12.45, -25.34) |
| 4:119661918 | T>N | B:714 | (-57.12, 8.53, -26.27) | |
| 4:119661916 | T>A | B:715 | (-53.00, 8.38, -24.94) | |
| 4:119661902 | rs199809201 | M>I | B:719 | (-51.21, 13.24, -13.29) |
| 4:119661891 | D>G | B:723 | (-49.63, 10.98, -4.42) | |
| 4:119661880 | rs200113050 | A>S | B:727 | (-54.33, 4.89, -8.12) |
| 4:119661870 | V>A | B:730 | (-55.78, 0.82, -16.90) | |
| 4:119661871 | rs545255356 | V>M | B:730 | (-55.78, 0.82, -16.90) |
| 4:119661855 | D>G | B:735 | (-56.00, -4.22, -31.33) | |
| 4:119661856 | D>N | B:735 | (-56.00, -4.22, -31.33) | |
| 4:119661852 | D>V | B:736 | (-54.94, -8.39, -33.09) | |
| 4:119661838 | D>N | B:741 | (-44.70, -17.66, -27.03) | |
| 4:119661832 | G>R | B:743 | (-47.81, -12.39, -24.43) | |
| 4:119661824 | L>F | B:745 | (-45.68, -6.99, -22.56) | |
| 4:119660438 | A>V | B:749 | (-44.84, 5.98, -17.96) | |
| 4:119660436 | rs146086094 | V>M | B:750 | (-44.79, 8.79, -15.06) |
| 4:119660426 | T>M | B:753 | (-41.58, 17.90, -12.10) | |
| 4:119660399 | R>Q | B:762 | (-41.23, 6.23, -11.54) | |
| 4:119660400 | R>W | B:762 | (-41.23, 6.23, -11.54) | |
| 4:119660376 | C>R | B:770 | (-51.19, -15.51, -22.99) | |
| 4:119660345 | S>N | B:780 | (-54.55, -15.93, -13.16) | |
| 4:119660336 | T>K | B:783 | (-60.99, -10.74, -6.39) | |
| 4:119660330 | A>G | B:785 | (-58.56, -6.29, -8.78) | |
| 4:119660331 | A>T | B:785 | (-58.56, -6.29, -8.78) | |
| 4:119660328 | rs367877257 | L>F | B:786 | (-61.71, -7.93, -10.71) |
| 4:119660317 | F>L | B:789 | (-62.77, -2.43, -13.33) | |
| 4:119659530 | F>L | B:795 | (-68.24, 4.50, -8.03) | |
| 4:119659529 | K>Q | B:796 | (-66.58, 6.97, -14.78) | |
| 4:119659451 | R>W | B:822 | (-70.89, -24.83, -14.04) | |
| 4:119659436 | S>G | B:827 | (-65.93, -30.55, -13.04) | |
| 4:119654066 | L>R | B:834 | (-72.46, -22.14, -7.03) | |
| 4:119654036 | rs76658950 | P>L | B:844 | (-69.31, -12.96, -4.59) |
| 4:119654028 | rs34510328 | M>V | B:847 | (-69.85, -7.47, -6.35) |
| 4:119654013 | K>Q | B:852 | (-74.76, -3.63, 0.20) | |
| 4:119654001 | rs142692250 | L>V | B:856 | (-74.37, 2.04, -6.48) |
| 4:119653998 | rs138684864 | L>I | B:857 | (-78.13, 2.28, -2.87) |
| 4:119653988 | rs375393177 | P>L | B:860 | (-83.08, 6.21, 2.27) |
| 4:119653989 | P>S | B:860 | (-83.08, 6.21, 2.27) | |
| 4:119653984 | E>D | B:861 | (-80.08, 8.54, 5.82) | |
| 4:119653982 | I>T | B:862 | (-76.71, 8.50, 2.94) | |
| 4:119653967 | rs143064954 | R>Q | B:867 | (-74.39, 9.08, -3.00) |
| 4:119653965 | A>T | B:868 | (-69.92, 12.21, -3.61) | |
| 4:119653956 | R>G | B:871 | (-67.62, 9.23, -7.34) | |
| 4:119653953 | rs565068897 | Q>E | B:872 | (-63.70, 11.82, -5.07) |
| 4:119653940 | T>I | B:876 | (-57.79, 7.52, -5.91) | |
| 4:119653928 | A>V | B:880 | (-55.24, -1.93, -0.44) | |
| 4:119653918 | Q>H | B:883 | (-59.89, -5.16, 0.83) | |
| 4:119653914 | rs201766693 | F>L | B:885 | (-64.41, 1.47, 1.31) |
| 4:119653908 | Y>H | B:887 | (-64.95, -7.43, 4.31) | |
| 4:119653901 | rs368876448 | Q>R | B:889 | (-60.21, -5.00, 9.77) |
| 4:119652658 | rs149063473 | T>M | B:895 | (-60.41, -11.90, 23.21) |
| 4:119652646 | COSM732853 | K>R | B:899 | (-47.53, -6.65, 26.29) |
| 4:119652637 | M>T | B:902 | (-49.16, -9.53, 16.42) | |
| 4:119652638 | M>V | B:902 | (-49.16, -9.53, 16.42) | |
| 4:119652623 | V>I | B:907 | (-64.32, -11.29, 12.69) | |
| 4:119652619 | rs550825173 COSM1664081 |
R>H | B:908 | (-67.73, -13.51, 8.11) |
| 4:119652620 | COSM284861 | R>C | B:908 | (-67.73, -13.51, 8.11) |
| 4:119652604 | R>H | B:913 | (-69.05, -13.79, 13.84) | |
| 4:119652605 | rs150351420 | R>C | B:913 | (-69.05, -13.79, 13.84) |
| 4:119652592 | E>G | B:917 | (-70.08, -11.07, 26.59) | |
| 4:119652585 | I>M | B:919 | (-65.20, -4.74, 23.16) | |
| 4:119652563 | rs199764116 | H>Y | B:927 | (-65.41, 6.02, 9.23) |
| 4:119652524 | L>V | B:940 | (-62.38, -4.13, 29.72) | |
| 4:119652519 | rs200473197 | I>M | B:941 | (-65.55, -0.25, 30.50) |
| 4:119652514 | G>A | B:943 | (-58.98, 0.36, 31.22) | |
| 4:119652490 | A>V | B:951 | (-73.64, 3.74, 31.61) | |
| 4:119649805 | rs201005070 | T>A | B:958 | (-64.99, 10.15, 20.39) |
| 4:119649783 | N>I | B:965 | (-50.78, -0.49, 32.23) | |
| 4:119649778 | Y>H | B:967 | (-56.34, -4.84, 28.44) | |
| 4:119649762 | R>K | B:972 | (-53.44, 4.52, 22.24) | |
| 4:119649744 | I>N | B:978 | (-55.26, -0.36, 11.97) | |
| 4:119649742 | Q>K | B:979 | (-54.13, 4.83, 10.63) | |
| 4:119649732 | R>T | B:982 | (-54.62, 2.31, 5.45) | |
| 4:119649719 | M>I | B:986 | (-59.25, 6.43, 10.77) | |
| 4:119644803 | I>T | B:990 | (-67.56, 5.28, 20.78) | |
| 4:119644791 | R>Q | B:994 | (-80.71, -2.36, 23.68) | |
| 4:119644767 | R>Q | B:1002 | (-76.89, -2.26, 12.72) | |
| 4:119644756 | V>I | B:1006 | (-70.93, -5.85, 4.52) | |
| 4:119644728 | S>F | B:1015 | (-78.72, -8.28, -0.16) | |
| 4:119644725 | S>C | B:1016 | (-77.50, -10.95, 2.21) | |
| 4:119644717 | rs532948364 | D>N | B:1019 | (-79.83, -13.16, -0.35) |
| 4:119644699 | H>Y | B:1025 | (-77.36, -20.59, -9.00) | |
| 4:119644696 | K>E | B:1026 | (-81.89, -17.56, -9.64) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:119686021 | COSM1618320 | H>L | B:412 | (-29.09, -7.87, -17.39) |
| 4:119685980 | COSM3714695 | V>L | B:426 | (-32.78, 11.46, -16.65) |
| 4:119678939 | COSM1671241 | I>K | B:454 | (-63.45, 32.90, 12.65) |
| 4:119678912 | COSM1671240 | C>Y | B:463 | (-52.46, 29.92, 11.44) |
| 4:119673862 | COSM1671239 | V>M | B:536 | (-42.61, 38.00, 7.70) |
| 4:119652620 | COSM284861 | R>C | B:908 | (-67.73, -13.51, 8.11) |